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Screening Metagenomic Data for Viruses Using the E-Probe Diagnostic Nucleic Acid Assay

October 2014 , Volume 104 , Number  10
Pages  1,125 - 1,129

A. H. Stobbe, W. L. Schneider, P. R. Hoyt, and U. Melcher

First, third, and fourth authors: Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater 74078; and second author: USDA-ARS, Foreign Disease-Weed Science Research Unit, Fort Detrick, MD 21702.

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Accepted for publication 24 March 2014.

Next generation sequencing (NGS) is not used commonly in diagnostics, in part due to the large amount of time and computational power needed to identify the taxonomic origin of each sequence in a NGS data set. By using the unassembled NGS data sets as the target for searches, pathogen-specific sequences, termed e-probes, could be used as queries to enable detection of specific viruses or organisms in plant sample metagenomes. This method, designated e-probe diagnostic nucleic acid assay, first tested with mock sequence databases, was tested with NGS data sets generated from plants infected with a DNA (Bean golden yellow mosaic virus, BGYMV) or an RNA (Plum pox virus, PPV) virus. In addition, the ability to detect and differentiate among strains of a single virus species, PPV, was examined by using probe sets that were specific to strains. The use of probe sets for multiple viruses determined that one sample was dually infected with BGYMV and Bean golden mosaic virus.

This article is in the public domain and not copyrightable. It may be freely reprinted with customary crediting of the source. The American Phytopathological Society, 2014.